PanKbase Data Library User Guide

Getting Started with the Data Library

The PanKbase Data Library at https://data.pankbase.org is your primary interface for browsing and searching all datasets in PanKbase. This guide will walk you through efficiently finding and accessing the data you need.

What You Can Find in the Data Library

The Data Library enables query and browsing of analysis resources created by PanKbase, including:

• Human Donors - Metadata on pancreas donors
• Biosamples - Pancreatic tissue and islet samples
• Experimental Assays - Details on performed experiments
• Analysis Results - Processed data and computational results
• Workflows - Analysis pipelines used to process data

Data Library Interface Overview

Main Search Interface

When you access the Data Library, you'll see:

• Search Bar (top): Enter keywords to search across all data types
• Filter Panel (left sidebar): Narrow results by category
• Results Grid (center): Browse matching datasets
• Sort Options (top right): Order results by relevance, date, or type
• View Toggle (top right): Switch between list and card views

Data Type Tabs

Click these tabs to focus on specific data types:

• Human Donors - Browse donor profiles and characteristics
• Biosamples - Find tissue samples and preparations
• Assays - Search experimental protocols and measurements
• Analysis Results - Access processed datasets and findings
• Workflows - Explore computational analysis pipelines

Step-by-Step Search Strategies

Strategy 1: Browse by Data Type

Best for: Exploring what's available in each category

1. Click a data type tab (Human Donors, Biosamples, etc.)
2. Scan the results to see available datasets
3. Use the filter panel to narrow by specific criteria
4. Click on items to view detailed information

Example Workflow - Finding T1D Donors:

1. Click "Human Donors" tab
2. Filter "Diabetes Status" → Select "Type 1 diabetes"
3. Filter "Age" → Choose age range of interest
4. Browse results and click donor IDs for details

Strategy 2: Keyword Search

Best for: Finding specific data or research topics

Effective Search Terms

• Disease-focused: "Type 1 diabetes", "autoantibody", "beta cell"
• Technical: "scRNA-seq", "single cell", "ATAC-seq", "proteomics"
• Sample-specific: "islets", "pancreas", "frozen"
• Donor-specific: "pediatric", "adult", "HbA1c", "C-peptide"

Search Tips

• Use quotes for exact phrases: "single cell RNA sequencing"
• Try different terms if initial search doesn't yield results
• Start broad then narrow with filters
• Check spelling - the search is case-sensitive for some terms

Example Search Workflow:

1. Enter "beta cell scRNA-seq" in search bar
2. Review results across all data types
3. Apply filters to narrow to specific donors or samples
4. Sort by "Most Recent" to see latest data

Strategy 3: Filter-First Approach

Best for: Finding data matching specific research criteria

1. Start with empty search (shows all data)
2. Apply filters systematically:
   • Diabetes Status → Choose disease state
   • Age Range → Select demographic
   • Sample Type → Pick tissue/preparation
   • Assay Type → Choose experimental method
3. Refine results by adding more specific filters
4. Save or bookmark useful filter combinations

Navigating Each Data Type

Human Donors Section

What You'll See

• Donor Cards showing key demographics and diabetes status
• Donor IDs (e.g., PKBDO7330CDCK) that link to detailed profiles
• Quick Stats like age, BMI, HbA1c on each card
• Available Data indicators showing what assays were performed

Key Filters

• Diabetes Status: T1D, T2D, gestational, MODY, control
• Age: Pediatric (<18), young adult (18-30), adult (30-65), elderly (>65)
• BMI Categories: Underweight, normal, overweight, obese
• HbA1c Ranges: Normal (<5.7%), prediabetic (5.7-6.4%), diabetic (≥6.5%)
• Autoantibody Status: GADA+, IA2+, IAA+, ZNT8+ positive/negative
• T1D Stage: At-risk, Stage 1, Stage 2, Stage 3, Unknown

Donor Detail Pages

Click any donor ID to see:

• Complete Demographics: Age, sex, BMI, ethnicity, genetics
• Medical History: Diabetes duration, treatments, family history
• Clinical Laboratory: HbA1c, C-peptide, autoantibody titers
• Donation Details: Cause of death, ischemia times, organ procurement
• Available Samples: Linked biosamples and their quality metrics
• Experimental Data: All assays performed on this donor's samples

List of fields collected for human donors: https://data.pankbase.org/standards/human-donor

Biosamples Section

What You'll See

• Sample Cards with tissue type, quality metrics, and processing details
• Quality Indicators: Viability percentages, purity scores, ischemia times
• Processing Info: Isolation center, culture conditions, preservation method
• Parent Donor: Link back to source donor information

Key Filters

• Sample Type: Islets, pancreatic tissue, cell lines, sorted cells
• Isolation Center: IIDP, HPAP, University of Alberta, nPOD, Prodo
• Viability Range: Set minimum viability thresholds
• Purity Range: Filter by islet purity percentages
• Ischemia Time: Cold and warm ischemia duration limits
• Culture Conditions: Fresh, cultured, cryopreserved
• Available Assays: Samples with specific experimental data

Sample Detail Pages

Click any sample to see:

• Quality Metrics: Pre/post-shipment viability, purity, yield (IEQ)
• Processing Timeline: Harvest, digestion, culture, shipping details
• Parent Relationships: Source donor, pooled samples, fractionated samples
• Experimental History: All assays performed on this sample
• Download Options: Associated data files and metadata

List of biosample fields: https://data.pankbase.org/standards/islet-biosample

Experimental Assays Section

What You'll See

• Assay Cards showing experimental method, sample size, and status
• Technology Platforms: 10x Genomics, Illumina, proteomics platforms
• Data Availability: Raw data, processed results, analysis ready files
• Quality Metrics: Cell counts, gene detection, success rates

Key Filters

• Assay Type: scRNA-seq, snATAC-seq, bulk RNA-seq, proteomics, imaging
• Platform: 10x Chromium, Smart-seq2, Visium, mass spectrometry
• Sample Size: Number of cells, samples, donors analyzed
• Data Status: Raw available, processed available, published
• Date Range: Recent experiments, historical data

Assay Detail Pages

Click any assay to see:

• Protocol Details: Step-by-step experimental procedures
• Technical Parameters: Sequencing depth, library preparation, quality control
• Sample Information: Source donors and biosamples used
• Data Files: Raw data, processed matrices, metadata files
• Analysis Results: Downstream analyses performed on this data

Analysis Results Section

What You'll See

• Analysis Cards showing computational results and interpretations
• Result Types: Cell type annotations, differential expression, pathway analysis
• Data Formats: Count matrices, statistical results, visualization files
• Publication Status: Published, preprint, manuscript in preparation

Key Filters

• Analysis Type: Cell clustering, differential expression, trajectory analysis
• Input Data: scRNA-seq based, snATAC-seq based, multi-modal
• Disease Focus: T1D vs control, T2D studies, developmental analysis
• Cell Types: Beta cells, alpha cells, immune cells, ductal cells
• Publication Status: Published, submitted, in progress

Analysis Detail Pages

Click any analysis to see:

• Methods Summary: Computational approaches used
• Input Datasets: Source experimental data analyzed
• Key Findings: Main biological conclusions
• Data Downloads: Processed results, figures, supplementary data
• Code Availability: Analysis scripts and computational notebooks

Workflows Section

What You'll See

• Workflow Cards showing analysis pipelines and computational methods
• Pipeline Steps: Data processing, quality control, analysis stages
• Software Tools: R packages, Python libraries, specialized software
• Reproducibility: Code availability, container images, parameter settings

Key Filters

• Workflow Type: Data processing, analysis, visualization, integration
• Input Data Type: scRNA-seq, snATAC-seq, proteomics, imaging
• Software Environment: R/Bioconductor, Python/scanpy, custom tools
• Complexity: Basic processing, advanced analysis, multi-modal integration

Workflow Detail Pages

Click any workflow to see:

• Pipeline Overview: Step-by-step processing description
• Software Requirements: Dependencies, versions, installation instructions
• Parameter Settings: Configuration files, optimization details
• Example Applications: Datasets processed with this workflow
• Code Repository: GitHub links, documentation, tutorials

Advanced Search Techniques

Cross-Reference Navigation

Link between data types efficiently:

1. Start with a donor → View their available samples
2. Click on samples → See what assays were performed
3. Browse assays → Find analysis results
4. Check workflows → Understand processing methods

Building Custom Searches

1. Combine multiple filters across categories
2. Use the search bar with filters for precise results
3. Save successful searches by bookmarking URLs
4. Export search results for offline reference

Research-Focused Searches

For specific research questions:

• "Find all T1D donors with single-cell data":
  • Filter Donors: Diabetes Status = T1D
  • Filter Assays: Type = scRNA-seq
  • Cross-reference donor IDs
• "Access processed beta cell expression data":
  • Filter Analysis Results: Cell Type = Beta cells
  • Filter by data format needed
  • Check publication status

Data Export and Access

Download Options

• Individual Files: Single datasets, metadata files
• Bulk Downloads: Multiple related files, complete studies
• Filtered Exports: Results matching your search criteria
• Formatted Data: CSV, Excel, HDF5, R/Python objects

External Links

• RRID Connections: Link to external resource databases
• Publication DOIs: Access related research papers
• GEO/SRA Links: Raw data in public repositories
• Collaboration Contacts: Connect with data generators

Data Integration

• API Access: Programmatic data retrieval
• Batch Processing: Large-scale data access
• Real-time Updates: Notification of new relevant data
• Citation Tracking: Proper attribution for data use

Support Options

• Email: Direct questions to PanKbase team at help@pankbase.org